It was designed to run outside of Quartus. You could just pare it down to the "set_global_assignment..." commands and run from Tools -> Tcl Scripts. That will modify the .qsf, and then just hit compile.
Did you do it in the GUI? What were the errors?
There are caveats, but this flow doesn't actually require you to create partitions, i.e. the Top level should always be in one, and SignalTap is kind of put into one on the side, so the caveats shouldn't really apply. (I think the web edition of Quartus II does not support partitions, but not positive). If you're interested, look at the Best Practices chapter:
http://www.altera.com/literature/hb/qts/qts_qii5v1.pdf